skpkg: update readme, license, delete instructions.txt, update module level comments

Author: zmx27

INSTRUCTIONS.txt

@@ -1,11 +1,29 @@
+BSD 3-Clause License
+
 Copyright (c) 2009-2025, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
-Use of this software is subject to and permitted only under a separate,
-written Use License granted by Columbia University.  If you or your employer
-is not a party to such an agreement, then your use of this software is
-prohibited.  If you don’t know whether or not your anticipated use is under
-a license, you must contact Prof. Simon Billinge at [email protected].
-Use of this software without a license is prohibited.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
 
-For more information please email Prof. Simon Billinge at [email protected]
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

LICENSE.rst

@@ -8,20 +8,30 @@
         :target: https://diffpy.github.io/diffpy.srxplanargui
         :height: 100px
 
-|PythonVersion|
+|PyPI| |Forge| |PythonVersion| |PR|
 
-|Black| |Tracking|
+|CI| |Codecov| |Black| |Tracking|
 
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
+.. |CI| image:: https://github.com/diffpy/diffpy.srxplanargui/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.srxplanargui/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.srxplanargui/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.srxplanargui
 
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.srxplanargui
+        :target: https://anaconda.org/conda-forge/diffpy.srxplanargui
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.srxplanargui/pulls
+
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srxplanargui
         :target: https://pypi.org/project/diffpy.srxplanargui/
 
-.. |PythonVersion| image:: https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.srxplanargui
+        :target: https://pypi.org/project/diffpy.srxplanargui/
 
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.srxplanargui/issues
@@ -42,7 +52,33 @@ If you use diffpy.srxplanargui in a scientific publication, we would like you to
 Installation
 ------------
 
-The preferred method is to be installed with `xpdfsuite` package or the wheel file.
+The preferred method is to use `Miniconda Python
+<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
+and install from the "conda-forge" channel of Conda packages.
+
+To add "conda-forge" to the conda channels, run the following in a terminal. ::
+
+        conda config --add channels conda-forge
+
+We want to install our packages in a suitable conda environment.
+The following creates and activates a new environment named ``diffpy.srxplanargui_env`` ::
+
+        conda create -n diffpy.srxplanargui_env diffpy.srxplanargui
+        conda activate diffpy.srxplanargui_env
+
+The output should print the latest version displayed on the badges above.
+
+If the above does not work, you can use ``pip`` to download and install the latest release from
+`Python Package Index <https://pypi.python.org>`_.
+To install using ``pip`` into your ``diffpy.srxplanargui_env`` environment, type ::
+
+        pip install diffpy.srxplanargui
+
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.srxplanargui/>`_. Once installed, ``cd`` into your ``diffpy.srxplanargui`` directory
+and run the following ::
+
+        pip install .
 
 This package also provides command-line utilities. To check the software has been installed correctly, type ::
 
@@ -57,12 +93,17 @@ To view the basic usage and available commands, type ::
 
         diffpy.srxplanargui -h
 
-Support
+Getting Started
+---------------
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.srxplanargui>`_ for tutorials and API references.
+
+Support and Contribute
 ----------------------
 
 If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srxplanargui/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srxplanargui/pulls>`_.
 
-Feel free to fork the project. To install diffpy.srxplanargui
+Feel free to fork the project and contribute. To install diffpy.srxplanargui
 in a development mode, with its sources being directly used by Python
 rather than copied to a package directory, use the following in the root
 directory ::
@@ -83,6 +124,8 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srxplanargui/blob/main/CODE-OF-CONDUCT.rst>`_.
+
 Contact
 -------
 

README.rst

@@ -49,7 +49,7 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-diffpy-srxplanargui = "diffpy.srxplanargui.srxguiapp:main"
+diffpy-srxplanargui = "diffpy.srxplanargui.srxplanargui_app:main"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}

pyproject.toml

@@ -7,8 +7,8 @@
 #
 # File coded by:    Xiaohao Yang
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See AUTHORS.rst for a list of people who contributed.
+# See LICENSE.rst for license information.
 #
 ##############################################################################
 

src/diffpy/srxplanargui/calibration.py

@@ -7,8 +7,8 @@
 #
 # File coded by:    Xiaohao Yang
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See AUTHORS.rst for a list of people who contributed.
+# See LICENSE.rst for license information.
 #
 ##############################################################################
 

src/diffpy/srxplanargui/datacontainer.py

@@ -7,8 +7,8 @@
 #
 # File coded by:    Xiaohao Yang
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See AUTHORS.rst for a list of people who contributed.
+# See LICENSE.rst for license information.
 #
 ##############################################################################
 """Provide help for SrXgui."""

src/diffpy/srxplanargui/help.py

@@ -7,8 +7,8 @@
 #
 # File coded by:    Xiaohao Yang
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See AUTHORS.rst for a list of people who contributed.
+# See LICENSE.rst for license information.
 #
 ##############################################################################
 """Plot the 2d image."""

src/diffpy/srxplanargui/imageplot.py

@@ -7,8 +7,8 @@
 #
 # File coded by:    Xiaohao Yang
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See AUTHORS.rst for a list of people who contributed.
+# See LICENSE.rst for license information.
 #
 ##############################################################################
 """Provide UI for srxplanar."""

src/diffpy/srxplanargui/live.py

@@ -7,8 +7,8 @@
 #
 # File coded by:    Xiaohao Yang
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See AUTHORS.rst for a list of people who contributed.
+# See LICENSE.rst for license information.
 #
 ##############################################################################